ReRep: Computational detection of repetitive sequences in genome survey sequences (GSS)

Background: Genome survey sequences (GSS) offer a preliminary global view of a genome since, unlike ESTs, they cover coding as well as non-coding DNA and include repetitive regions of the genome. A more precise estimation of the nature, quantity and variability of repetitive sequences very early in a genome sequencing project is of considerable importance, as such data strongly influence the estimation of genome coverage, library quality and progress in scaffold construction. Also, the elimination of repetitive sequences from the initial assembly process is important to avoid errors and unnecessary complexity. Repetitive sequences are also of interest in a variety of other studies, for instance as molecular markers. Results: We designed and implemented a straightforward pipeline called ReRep, which combines bioinformatics tools for identifying repetitive structures in a GSS dataset. In a case study, we first applied the pipeline to a set of 970 GSSs, sequenced in our laboratory from t...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Thomas D. Otto, Leonardo H. F. Gomes, Marcelo Alves-Ferreira, Antonio Basílio de Miranda, Wim M. Degrave
• Keywords: BMCBI 2008, Genome, Gss Dataset, Repetitive Sequences